Simon Elsässer, Karolinska Institutet (2023)

Profile plots of promoters, enhancders and significant peaks determined by DESeq2.

bw_dir <- "/Volumes/DATA/DATA/Puck/bigwig/"

library("wigglescout")
library("ggpubr")
library("ggplot2")
library("DESeq2")
library("dplyr")
library("ggrastr")

clean <- function (fn) {
  fn <- gsub(pattern = ".+/", "", x = fn)
  fn <- gsub(pattern = ".mm9.+", "", x = fn)
  fn <- gsub(pattern = ".mm39.+", "", x = fn)
  fn <- gsub(pattern = "_S.+", "", x = fn)
  fn <- gsub(pattern = "_combined.+", "", x = fn)
  fn <- gsub(pattern = "G4 CnT ", "", x = fn)
  fn <- gsub(pattern = "_batch2", "", x = fn)
  fn <- gsub(pattern = "-", " ", x = fn)
  fn <- gsub(pattern = "_", " ", x = fn)
  fn <- gsub(pattern = " HA ", " ", x = fn)
  fn <- gsub(pattern = "D1D6", "FANCJ-/-", x = fn)
  fn <- gsub(pattern = "P2D2", "DHX36-/-", x = fn)
  fn <- gsub(pattern = "P3D4", "FANCJ-/-DHX36-/-", x = fn)
  return(fn)
}

BWs <- paste0(bw_dir,list.files(bw_dir,pattern="G4_.+R..bw"))

mypal <-c("cornflowerblue","orange","red2","#505050")
mypal3 <-c("cornflowerblue","cornflowerblue","cornflowerblue","orange","orange","orange","red2","red","red2","black","black","black")
mypal2 <-c("cornflowerblue","cornflowerblue","orange","orange","red2","red","black","black")

DHX36-/- vs WT significant peaks

FANCJ-/- vs WT significant peaks

DKO-/- vs WT significant peaks

DKO-/- vs WT significant peaks

DKO-/- vs WT significant peaks

#non-significant Peaks

Active Promoters

Active Enhancers

cov_proHi <- bw_loci(BWs, loci = "../genome/genes_hi_lt10kb.mm39.bed",labels = clean(BWs))

df <- as.data.frame(cov_proHi)[6:9]
colnames(df) <- c("FANCJ","DHX36","DKO","WT")
ggscatter(df,x ="WT",y="DKO",size = 0.8, alpha=0.5) + geom_abline(slope = 1, intercept = 0, linetype="dashed", size=0.1)

R loops

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